Upload Data

Expression Data

An unlabelled peptide expression data file called “pep_edata.csv” was uploaded to pmart. The column that designates unique molecules was marked as “Mass_Tag_ID”. The original scale of the data was raw intensity and was changed to log2. The value to denote missing data was “NA” and the expression data was not already normalized.

Biomolecule Information

An associated biomolecule information file was also uploaded called “pep_emeta.csv” and the protein identifier column was designated as “Protein”.

Sample Information

An associated sample information file was also uploaded called “pep_fdata.csv”. Trimmed sample names were not used. The column in the sample information file which indicates sample names was designated as “SampleID”.

Group Samples

Grouping Information

This table summarizes all the user specified main effects or covariates in pmart. The “Selected Column Name” denotes the name of the column in the sample information file assigned as a main effect or covariate.

Main Effect or Covariate Selected Column Name
First Main Effect Condition
Second Main Effect None selected
First Covariate None selected
Second Covariate None selected

Number of Samples per Main Effects

Data Summary

Summary Table

The first column in the table below denotes a property of the peptide data, and the “Data” column states that property’s value.

Data
Class pepData
Unique SampleIDs (f_data) 10
Unique Mass_Tag_IDs (e_data) 13022
Unique Proteins (e_meta) 1736
Missing Observations 35221
Proportion Missing 0.27
Samples per group: Infection 7
Samples per group: Mock 3

Missing Value Table

In the table below, the first column denotes the sample and the second is the missing number of observations. The third column represents the second as a percentage of the total number of observations for that sample.

Missing Observations Proportion Missing
Infection1 2620 0.201
Infection3 3446 0.265
Infection4 3978 0.305
Infection6 3534 0.271
Infection7 2896 0.222
Infection8 6015 0.462
Infection9 4953 0.380
Mock1 2680 0.206
Mock2 2550 0.196
Mock3 2549 0.196

Filter

Filters were applied.

Summary of Applied Filters

Filter Type Parameters
Molecule Filter Biomolecule Molecule Number Min: 2
CV Filter Biomolecule Max CV: 150
imd-ANOVA Filter Biomolecule ANOVA Min: 2 & G-test Min: 3
Proteomics Filter Biomolecule Peptide Number Min: 2 & Remove Degenerates: Yes
rMD Filter Sample P-Value Threshold: 0.001 & Outlier Metrics: MAD, Kurtosis, Skewness, Correlation
Custom Filter Sample The custom filter removedthe following sample(s): Infection5

Molecule Filter

A molecule filter was applied to the data, removing Mass_Tag_IDs not having at least 2 samples.

CV Filter

A coefficient of variation (CV) filter was applied to the data removing Mass_Tag_IDs with a CV greater than 150

imd-ANOVA Filter

An ANOVA filter was applied to the data, removing Mass_Tag_IDs not having at least 2 non-missing values per group. Additionaly, an IMD (independence of missing data) filter was applied to the data, removing Mass_Tag_IDs not having at least 3 non-missing values in at least one of the groups.

Proteomics Filter

A degenerate peptide filter was applied to the data, identifying Mass_Tag_IDs mapping to more than one protein. Additionally, a protein filter was applied to the data, identifying proteins not having at least 2 Mass_Tag_IDs mapping to them.

rMD Filter

A robust Mahalanobis distance (rMD) filter was applied to the data, removing SampleIDs with an associated rMD-associated p-value less than 0.001.

Custom Filter

The custom filter removedthe following sample(s): Infection5

Normalization

Peptide data was normalized.

SPANS

SPANS was run to determine optimum normalization parameters.

Manual

Manual normalization was used to normalize the data.

Attribute Value
Subset Function los
Subset Parameters los: 0.05
Normalization Function mean

Statistical Analysis

The analysis step was run.

The following groups were compared: Infection_vs_Mock. Reported below are the parameters used in the statistical analysis, followed by the number of siginificant biomolecules for each comparison.

Attribute Value
Test Method anova
Multiple Comparison Adjustment holm
Significance Threshold 0.05
Comparison Up_total Down_total Up_anova Down_anova Up_gtest Down_gtest
Infection_vs_Mock Infection_vs_Mock 1509 2742 1509 2742 0 0